I want to learn how to create 3D games using Blender and Godot. First Step would be what steps would I need to create a universe?
Sounds like you want to make a game, and really you just want to make some assets.  I'm not sure this it's possible to really answer the high level of complexity here but I can give you some overviews.   

LOD is Level of Detail, and it means that you create at least three versions of a planet (Or any other object): A small four point plane with an image mapped to it for when you are too far away to care what it looks like, a low poly sphere with a texture mapped onto it for medium range, And a high detail version which includes multiple sphere's with transparency set on the outer spheres to represent clouds and atmospheres.  

Use camera cuts to show show them landing on the surface, and then load up an area with natural boundaries to keep them contained in that area.

As for your universe and the planetary systems, there are quite a lot of ways to accomplish this.  I'm just going to suggest A way. 

Create a few basic models of planets and moons together as groups.  Parent them to an empty object at the center of your planets.  Add Array modifiers to the moon to get more than one moon. Use drivers on the rotation of the empty to rotate the moons, and a driver on the moon to turn the base moon. Try playing with array modifiers stacked on array modifiers.

Once you have some variations of planets, you create a subdivided plane and add particles to it.  The particles can be groups and you can add your planet groups to the particle field.  Make sure you use the outline view of the plane to turn rendering of the plane off.  You can add more planes with different geometry to cluster or distribute other planet groups.  Remove geometry in the center of your plane to make room for the black hole.

Use a very large sphere UV mapped with stars with the normals flipped inside to represent deep space.

Use the camera depth to trigger your LOD detail for the planets and moons.

Assuming this is for a game, you CAN use the blender game engine, but you should probably leave it to Unity or the Unreal Engine (UE4) for the actual game environment.